Alignments for a candidate for xylA in Alkalitalea saponilacus SC/BZ-SP2

GapMind for catabolism of small carbon sources

Alignments for a candidate for xylA in Alkalitalea saponilacus SC/BZ-SP2

Align Xylose isomerase (EC 5.3.1.5) (characterized)
to candidate WP_079558612.1 CDL62_RS00405 xylose isomerase

Query= reanno::Cola:Echvi_1876
         (437 letters)



>NCBI__GCF_002201795.1:WP_079558612.1
          Length = 442

 Score =  677 bits (1746), Expect = 0.0
 Identities = 314/436 (72%), Positives = 371/436 (85%)

Query: 2   SKTYFPGIEKIKYEGRDSKNPFAFKFYDENKVVAGKTMKEHFKFAIAYWHSFNATGDDPF 61
           +K YFPGI +IK+EG++SKNP AFK+Y+ ++VV GKTMKEH +FA++YWH+F   G DPF
Sbjct: 7   NKEYFPGIGEIKFEGKESKNPLAFKWYNADQVVGGKTMKEHLRFAVSYWHTFCGLGGDPF 66

Query: 62  GPGTKTFVWDQAEDALQRAKDKMDAAFEFITKIGAPYYCFHDVDLIDEGSTIEEYESRMK 121
           GPGT+ + W  A DA++ AK+KMDAAFEF TK+G PYYCFHD+DL+ EGS+I EYE  M+
Sbjct: 67  GPGTQKYPWLGAGDAIEEAKNKMDAAFEFFTKLGVPYYCFHDIDLVSEGSSIAEYEKNMQ 126

Query: 122 AITEYAKQKQVETGVKLLWGTANVFSNPRYMNGASTNPDFDVVSWAATQVKNSIDATIAL 181
           +I +YAK KQ  +GVKLLWGTANVFSNPRYMNGASTNPDF  +++A TQVKN+IDATIAL
Sbjct: 127 SIVDYAKAKQAASGVKLLWGTANVFSNPRYMNGASTNPDFAALAYAGTQVKNAIDATIAL 186

Query: 182 GGENYVFWGGREGYMSLLNTDMKRETEHLAKFLTMARDYGRKQGFKGNFLIEPKPMEPTK 241
           GGE Y FWGGREGYMSLLNT+MKRE EH+ +FL+MARDY RKQGFKG F IEPKPMEPTK
Sbjct: 187 GGEGYTFWGGREGYMSLLNTNMKRELEHMGRFLSMARDYARKQGFKGCFYIEPKPMEPTK 246

Query: 242 HQYDYDSATVVGFLRHYGLDKDFKLNIEVNHATLAGHTFQHELQVAADAGLLGSIDANRG 301
           HQYD+DSATV+GFLR YGL+KDFK+NIEVNHATLA HTFQHELQVAADAG+LGSIDANRG
Sbjct: 247 HQYDFDSATVIGFLRQYGLEKDFKVNIEVNHATLASHTFQHELQVAADAGMLGSIDANRG 306

Query: 302 DYQNGWDTDQFALNLQELTESLLVILEAGGLQGGGVNFDAKLRRNSTDLDDLFHAHIGSM 361
           DYQNGWDTDQF +N+ E  E++LVILEAGG Q GGVNFDAK+RRNSTDL+D+F AH+ +M
Sbjct: 307 DYQNGWDTDQFPINIYETAEAMLVILEAGGFQTGGVNFDAKIRRNSTDLEDIFIAHVSAM 366

Query: 362 DAFARALLIANDILEQSEYKALRKKRYASFDGGKGKEFEEGKLTLEDLREHAIATGEPAS 421
           D FAR+L+IA+ +L  S+YK +R  RYAS+D GKG EFE GKLTLEDLR  A   GEPA 
Sbjct: 367 DVFARSLVIADKVLSDSDYKKMRAARYASYDSGKGAEFEAGKLTLEDLRNFAAQNGEPAR 426

Query: 422 TSGKQEMYENIINQYI 437
            SGKQE+YE +IN YI
Sbjct: 427 ISGKQELYEQLINLYI 442


Lambda     K      H
   0.317    0.135    0.400 

Gapped
Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 1
Number of Hits to DB: 681
Number of extensions: 19
Number of successful extensions: 1
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 1
Number of HSP's successfully gapped: 1
Length of query: 437
Length of database: 442
Length adjustment: 32
Effective length of query: 405
Effective length of database: 410
Effective search space:   166050
Effective search space used:   166050
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.6 bits)
S2: 51 (24.3 bits)

Align candidate WP_079558612.1 CDL62_RS00405 (xylose isomerase)
to HMM TIGR02630 (xylA: xylose isomerase (EC 5.3.1.5))

# hmmsearch :: search profile(s) against a sequence database
# HMMER 3.3.1 (Jul 2020); http://hmmer.org/
# Copyright (C) 2020 Howard Hughes Medical Institute.
# Freely distributed under the BSD open source license.
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
# query HMM file:                  ../tmp/path.carbon/TIGR02630.hmm
# target sequence database:        /tmp/gapView.1822083.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR02630  [M=435]
Accession:   TIGR02630
Description: xylose_isom_A: xylose isomerase
Scores for complete sequences (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Sequence                             Description
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
   2.2e-210  685.0   1.7   2.5e-210  684.8   1.7    1.0  1  NCBI__GCF_002201795.1:WP_079558612.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_002201795.1:WP_079558612.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  684.8   1.7  2.5e-210  2.5e-210       1     435 []      10     442 .]      10     442 .] 0.99

  Alignments for each domain:
  == domain 1  score: 684.8 bits;  conditional E-value: 2.5e-210
                             TIGR02630   1 ffeeiekvkyeGkdsknplafkyynpeeviegkkmkdhlrfavayWhtlaaegaDpfGagtaerpwdkeltda 73 
                                           +f++i ++k+eGk+sknplafk+yn+++v+ gk+mk+hlrfav+yWht++  g+DpfG gt+++pw     da
  NCBI__GCF_002201795.1:WP_079558612.1  10 YFPGIGEIKFEGKESKNPLAFKWYNADQVVGGKTMKEHLRFAVSYWHTFCGLGGDPFGPGTQKYPWL-GAGDA 81 
                                           8*****************************************************************9.67*** PP

                             TIGR02630  74 ldkakakvdaafelleklgveyycfhDvDiapegaslketnanldeivdllkekqketgvklLWgtanlfshp 146
                                           +++ak+k+daafe+++klgv+yycfhD+D+++eg+s++e+++n+++ivd++k kq+++gvklLWgtan+fs+p
  NCBI__GCF_002201795.1:WP_079558612.1  82 IEEAKNKMDAAFEFFTKLGVPYYCFHDIDLVSEGSSIAEYEKNMQSIVDYAKAKQAASGVKLLWGTANVFSNP 154
                                           ************************************************************************* PP

                             TIGR02630 147 ryvaGaatspdadvfayaaaqvkkalevtkklggenyvfWGGreGyetLlntdlkleldnlarflklavdyak 219
                                           ry++Ga+t+pd+  +aya++qvk+a+++t  lgge+y fWGGreGy++Llnt++k+el++++rfl++a+dya+
  NCBI__GCF_002201795.1:WP_079558612.1 155 RYMNGASTNPDFAALAYAGTQVKNAIDATIALGGEGYTFWGGREGYMSLLNTNMKRELEHMGRFLSMARDYAR 227
                                           ************************************************************************* PP

                             TIGR02630 220 kigfkgqlliePkPkePtkhqyDfDaatvlaflkkydLdkdfklnieanhatLaghtfehelrvarelgllGs 292
                                           k gfkg ++iePkP+ePtkhqyDfD+atv++fl++y+L+kdfk+nie+nhatLa htf+hel+va+++g+lGs
  NCBI__GCF_002201795.1:WP_079558612.1 228 KQGFKGCFYIEPKPMEPTKHQYDFDSATVIGFLRQYGLEKDFKVNIEVNHATLASHTFQHELQVAADAGMLGS 300
                                           ************************************************************************* PP

                             TIGR02630 293 iDanrgdlllGWDtDefptdvyeatlamyevlkagglakGGlnfdakvrresldaeDlllahiagmDafargl 365
                                           iDanrgd+++GWDtD+fp+++ye++ am+ +l+agg+++GG+nfdak+rr+s+d eD+++ah+++mD far+l
  NCBI__GCF_002201795.1:WP_079558612.1 301 IDANRGDYQNGWDTDQFPINIYETAEAMLVILEAGGFQTGGVNFDAKIRRNSTDLEDIFIAHVSAMDVFARSL 373
                                           ************************************************************************* PP

                             TIGR02630 366 kvaaklledgaleklveeryesfdseiGkeieegkadleelekyalekeeeaekksgrqelleslinkyl 435
                                            +a k+l d+ ++k+ + ry+s+ds+ G+e+e+gk +le+l + a++++e +++ sg+qel+e+lin y+
  NCBI__GCF_002201795.1:WP_079558612.1 374 VIADKVLSDSDYKKMRAARYASYDSGKGAEFEAGKLTLEDLRNFAAQNGE-PARISGKQELYEQLINLYI 442
                                           ************************************************97.****************997 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (435 nodes)
Target sequences:                          1  (442 residues searched)
Passed MSV filter:                         1  (1); expected 0.0 (0.02)
Passed bias filter:                        1  (1); expected 0.0 (0.02)
Passed Vit filter:                         1  (1); expected 0.0 (0.001)
Passed Fwd filter:                         1  (1); expected 0.0 (1e-05)
Initial search space (Z):                  1  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.00
# Mc/sec: 27.31
//
[ok]

This GapMind analysis is from Sep 24 2021. The underlying query database was built on Sep 17 2021.

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About GapMind

Each pathway is defined by a set of rules based on individual steps or genes. Candidates for each step are identified by using ublast (a fast alternative to protein BLAST) against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer with enzyme models (usually from TIGRFam). Ublast hits may be split across two different proteins.

A candidate for a step is "high confidence" if either:

ublast finds a hit to a characterized protein at above 40% identity and 80% coverage, and bits >= other bits+10.
- (Hits to curated proteins without experimental data as to their function are never considered high confidence.)
HMMer finds a hit with 80% coverage of the model, and either other identity < 40 or other coverage < 0.75.

where "other" refers to the best ublast hit to a sequence that is not annotated as performing this step (and is not "ignored").

Otherwise, a candidate is "medium confidence" if either:

ublast finds a hit at above 40% identity and 70% coverage (ignoring otherBits).
ublast finds a hit at above 30% identity and 80% coverage, and bits >= other bits.
HMMer finds a hit (regardless of coverage or other bits).

Other blast hits with at least 50% coverage are "low confidence."

Steps with no high- or medium-confidence candidates may be considered "gaps." For the typical bacterium that can make all 20 amino acids, there are 1-2 gaps in amino acid biosynthesis pathways. For diverse bacteria and archaea that can utilize a carbon source, there is a complete high-confidence catabolic pathway (including a transporter) just 38% of the time, and there is a complete medium-confidence pathway 63% of the time. Gaps may be due to:

our ignorance of proteins' functions,
omissions in the gene models,
frame-shift errors in the genome sequence, or
the organism lacks the pathway.

GapMind relies on the predicted proteins in the genome and does not search the six-frame translation. In most cases, you can search the six-frame translation by clicking on links to Curated BLAST for each step definition (in the per-step page).

For more information, see:

the paper from 2019 on GapMind for amino acid biosynthesis
the 2024 update on GapMind for amino acid biosynthesis
the paper from 2022 on GapMind for carbon sources
the source code
instructions for running GapMind on your computer

If you notice any errors or omissions in the step descriptions, or any questionable results, please let us know

by Morgan Price, Arkin group, Lawrence Berkeley National Laboratory

GapMind for catabolism of small carbon sources